Biosynthetic gene cluster identification in plasmids and characterization of plasmids from animal-associated microbiota
Date
2021-11-24
Authors
Journal Title
Journal ISSN
Volume Title
Publisher
ORCID
Type
Thesis
Degree Level
Masters
Abstract
Individual bacteria in complex microbial communities can acquire and accumulate new traits.
These traits are reflective of their environment, being niche-specific. A major player in trait
sharing is horizontal gene transfer (HGT). Plasmids, extrachromosomal DNA molecules, have
a role in HGT and can change the host’s phenotype. Considering the transformative role of
plasmids in bacterial lifestyle, we investigated the prevalence, distribution and products of
biosynthetic gene clusters (BGCs) present in plasmids. Sequences available on the National
Center for Biotechnology Information (NCBI) database (n=101 416) were run through two
bioinformatic pipelines for BGC detection that apply different approaches, deepBGC and
antiSMASH (antibiotics and secondary metabolites analysis shell). The highest percentage of
plasmids with BGCs was detected in Actinobacteria but, apart from Chlamidiae and
Tenericutes, all phyla had BGCs in their plasmids, with predictions varying according to the
software used. The BGCs identified comprised a range of classes, indicating that plasmid encoded BGCs could be leveraged for the discovery of new molecules. In order to apply that
concept to real-life examples, plasmids were isolated from animal-associated microbial
communities and characterized. Plasmids from Escherichia coli isolated from wild birds
(n=36) were screened for phenotypes of interest in human and animal health. Seven isolates
displayed plasmid-encoded antibiotic resistance. Taxonomic identification of the hosts of
plasmids isolated from bovid-associated microbiomes (n=38) was determined via 16S rRNA
gene, and placed the majority of the isolated in the phylum Firmicutes, apart from a single
Klebsiella pneumoniae isolate. Twelve plasmids were sequenced. Three plasmids from
different hosts (pRAM-12, pRAM-19-2 and pRAM-30-2) shared 100% nucleotide sequence
and a gene cluster for the bacteriocin cloacin. Two of those hosts shared not one, but two
plasmids, pRAM-19-1 and pRAM-30-1, despite being in different phyla. This highlights the
intimacy of gene sharing and the importance of HGT. pRAM-28 and pRAM-21 shared a
plasmid that harbors the BGC for the bacteriocin aureocin A70, the only four peptide
bacteriocin known to date. Additional analysis revealed two putative novel lanthipeptide gene
clusters in pRAM-2. These results suggest that the plasmidome is a neglected source of
secondary metabolites with the potential for molecule discovery. Furthermore, it can be
leveraged to study genetic exchange in a community and how plasmid-encoded featured can
mediate interactions in a microbiome.
Description
Keywords
Plasmids, microbiome, biosynthetic gene clusters, bioinformatics.
Citation
Degree
Master of Science (M.Sc.)
Department
Veterinary Microbiology
Program
Veterinary Microbiology